How can I upload files to my multisite network sites I created with WP Empire Builder? The folder structure seems confusing

Solution

This is a well known WP multisite limitation (not caused by WP Empire Builder). It doesn't allow you uploading custom files to a root folder of a child site or to a custom folder other than "files".
 
The "files" folder of each site could be found at this path: wp-content/blogs.dir/{site_id}/files, where {site_id} is child site's ID number.
 

 
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